#NEXUS
[written Tue Aug 25 00:32:43 BRT 2015 by Mesquite  version 3.04 (build 725) at fernando-HP-Pavilion-15-Notebook-PC/127.0.1.1]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=13;
	TAXLABELS
		'Caldanaerobacter subterraneus pacificus_EEB75482.1' 'Caldanaerobacter subterraneus tengcongensis_NP_624062.1' 'Caldanaerobacter subterraneus yonseiensis_ERM91218.1' 'Caldicellulosiruptor bescii YP_002573898.1' 'Caldicellulosiruptor hydrothermalis YP_003991814.1' 'Caldicellulosiruptor kronotskyensis YP_004023322.1' Thermoanaerobacter_ethanolicus_EGD52029.1 Thermoanaerobacter_siderophilus_EIW00539.1 Thermoanaerobacter_siderophilus_EIW00263.1 Thermoanaerobacter_thermohydrosulfuricus_EMT39667.1 'Thermoanaerobacter wiegelii YP_004818845.1' 'Thermoanaerobacter wiegelii YP_004818850.1' 'Thermoanaerobacter wiegelii YP_004820398.1' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=386;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'Caldanaerobacter subterraneus pacificus_EEB75482.1'     ---------------------------------MIVQNLRGGIYMVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVILGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAALTPVGEPLSTIVVSKLHADFFYLARLIGIEIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSEILYWANTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
	'Caldanaerobacter subterraneus tengcongensis_NP_624062.1' --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSVELFFHIFKNPLIYYITLAVLIAGLIFALLKEKLKIGVEKVADKISLRLFAFIIIVILGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAALTPVGEPLATIVVSKLHADFFYLARLIGIEIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIREVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSEILYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
	'Caldanaerobacter subterraneus yonseiensis_ERM91218.1'   --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFRAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPVIDLYIVKMKSEILYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
	'Caldicellulosiruptor bescii YP_002573898.1'             --------------------------------------------MIAGLIILLLVILFIPFLVKAVEHNLEYFLFVMGIIGVIISKQMNLKLFEHILQNKLLYYITFAVLIAGMLFFFFRNKINRLIDVLTNKISIQIFTFIIIVILGLSSSFITAIIASLLLTEIMHHTPLERNTKLKVIVLACFAIGFGAALTPVGEPLATITISKLKADFFYLARAIGFEIIITILLMAFLAALIVKKANKV-DKDEYIENTEGIKDVFLRAFKVFVFVFALELLGTAFKPLIDLYIIKLDAKILYWVNMISAIVDNATLAAAEVSKEMTNEQVRAIILGMIISGGMLIPGNIPNIISAGKFKIKSKEWAKIGVPMGLILMVIYFIMVFIVKV
	'Caldicellulosiruptor hydrothermalis YP_003991814.1'     --------------------------------------------MITGLIVLLLIILFLPFFVKAVEHNLEYFLFIMGIIGVIISKQMSLDLIEHIFKNRLLYYITFAVLIAGMLFFFFRDKINRMIELLTHKISIQLFIFIVIIMLGLSSSFITAIIASLLLTEIMHHMPLDRNTKLKVIVLACFAIGFGAALTPVGEPLATITISKLKADFFYLARAIGLEIIITILLMACLAALVVKKANKI-DKDEFIENTEGIKDVFLRAFKVFIFVFALELLGTAFKPLIDLYIIKLDAKILYWVNMISAIVDNATLAAAEISKDMTNEQVRAIILGMIVSGGMLIPGNIPNIISAGKFKIKSKEWAKIGVPIGLILMAVYFVLVFVLKV
	'Caldicellulosiruptor kronotskyensis YP_004023322.1'     --------------------------------------------MIAGLIILLLVILFIPFLVKAVEHNLEYFLFVMGIIGVIISKQMNLKLFEHILQNKLLYYITFAVLIAGMLFFFFRNKINRLIEVLTNKISIQIFTFIIIVILGLSSSFITAIIASLLLTEIMHHTPLDRNTKLKVIVLACFAIGFGAALTPVGEPLATITISKLKADFFYLARAIGFEIIITILLMAFLAALIVKKANKV-DKDEYIENTEDIKDVFLRAFKVFVFVFALELLGTAFKPLIDLYIIKLDAKILYWVNMISAIVDNATLAAAEVSKEMTNEQVRAIILGMIISGGMLIPGNIPNIISAGKFKIKSKEWAKIGVPMGLILMVIYFIMVFIVKV
	Thermoanaerobacter_ethanolicus_EGD52029.1                --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
	Thermoanaerobacter_siderophilus_EIW00539.1               --------------------------------------------MVIALFVILVLILLLPFMVKQVEHNLEYFLFTMGIISVIVSKQFSIELFLHIFKNPLIYYITLAVLIAGLVFTLFKEKLKIGMEKITDKISLRLFAFIIIVFLGLMSSIITAIIASLVLVEIVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLNADFFYLARLIGIDVIIAVVILGLIGAFFAKRESGTTNFMKDIDANENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPAMTQEQVRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGGILLLVYYVVLFVI--
	Thermoanaerobacter_siderophilus_EIW00263.1               MSMPLSYEYYTTKTLCNTPGAPQKLMFVFIYSFVSKYILQGGIYMVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
	Thermoanaerobacter_thermohydrosulfuricus_EMT39667.1      --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKVNLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
	'Thermoanaerobacter wiegelii YP_004818845.1'             --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSVELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVA--VSLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGVDIIIAILVLGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPVIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
	'Thermoanaerobacter wiegelii YP_004818850.1'             --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVAEKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENTKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
	'Thermoanaerobacter wiegelii YP_004820398.1'             MSMPLSYEYYTTKTLCNTPGAPQKLMFVFIYSFVSKYILQGGIYMVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  386;

END;

BEGIN NOTES;

	TAXABITS   TAXA = Taxa NAME = newlyAddedTaxon on =  1 -  13;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  386;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  386;
END;

BEGIN TREES;
	Title 'Trees from "O163_11565.tre"';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		n0 'Caldanaerobacter subterraneus pacificus_EEB75482.1',
[1] 		n1 'Caldanaerobacter subterraneus tengcongensis_NP_624062.1',
[2] 		n2 'Caldanaerobacter subterraneus yonseiensis_ERM91218.1',
[3] 		n3 'Caldicellulosiruptor bescii YP_002573898.1',
[4] 		n4 'Caldicellulosiruptor hydrothermalis YP_003991814.1',
[5] 		n5 'Caldicellulosiruptor kronotskyensis YP_004023322.1',
[6] 		n6 Thermoanaerobacter_ethanolicus_EGD52029.1,
[7] 		n7 Thermoanaerobacter_siderophilus_EIW00539.1,
[8] 		n8 Thermoanaerobacter_siderophilus_EIW00263.1,
[9] 		n9 Thermoanaerobacter_thermohydrosulfuricus_EMT39667.1,
[10] 		n10 'Thermoanaerobacter wiegelii YP_004818845.1',
[11] 		n11 'Thermoanaerobacter wiegelii YP_004818850.1',
[12] 		n12 'Thermoanaerobacter wiegelii YP_004820398.1';
	TREE tree_1 = (((((((n9:0.002957,(n6:0.000001,n11:0.00296)0.0000:0.000001)0.0000:0.000001,n8:0.000001)0.0000:0.000001,n12:0.000001)0.7430:0.003025,((n1:0.008904,n0:0.005918)0.9270:0.008958,n2:0.005866)0.7650:0.002983)0.4110:0.00603,n10:0.008867)0.8640:0.039017,n7:0.069473)1.0000:0.2591685,(n4:0.046194,(n3:0.005827,n5:0.002963)0.9490:0.072968)1.0000:0.2498465)root;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1440473563607;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 6090546851217445804;
			tell It;
				setDefaultOrder  6 5 7 11 10 12 1 9 3 0 8 2 4;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 1173296182098455485;
			mqVersion 304;
			checksumv 0 3 716612060 null  getNumChars 386 numChars 386 getNumTaxa 13 numTaxa 13   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 4.484281661366E13 sumSquares 4.484281661366E13 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 234;
			setPopoutState 300;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 700 464;
			setLocation 51 24;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #6090546851217445804 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #6090546851217445804;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 466 392;
					setLocation 51 24;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam;
					endTell;
					setActive;
				endTell;
				showWindow;
				getEmployee #mesquite.lists.ColorTaxon.ColorTaxon;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
				tell It;
					togglePanel off;
				endTell;
			endTell;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #1173296182098455485 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 466 392;
					setLocation 51 24;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					colorCells  #mesquite.charMatrices.ColorByState.ColorByState;
				tell It;
					setStateLimit 9;
					toggleUniformMaximum on;
				endTell;
					colorRowNames  #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
					colorColumnNames  #mesquite.charMatrices.CharGroupColor.CharGroupColor;
					colorText  #mesquite.charMatrices.NoColor.NoColor;
					setBackground White;
					toggleShowNames on;
					toggleShowTaxonNames on;
					toggleTight off;
					toggleThinRows off;
					toggleShowChanges off;
					toggleSeparateLines off;
					toggleShowStates on;
					toggleAutoWCharNames off;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					toggleBirdsEye off;
					toggleShowPaleGrid off;
					toggleShowPaleCellColors off;
					toggleShowPaleExcluded off;
					togglePaleInapplicable on;
					toggleShowBoldCellText off;
					toggleAllowAutosize off;
					toggleColorsPanel off;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
				endTell;
				showWindow;
				getWindow;
				tell It;
					forceAutosize;
				endTell;
				getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
				tell It;
					togglePanel off;
				endTell;
				getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
				tell It;
					autotabOff;
				endTell;
				getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
				tell It;
					gapCosts 8 3 2 2;
					subCosts  5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5;
				endTell;
				getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		endTell;
end;